RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets

Table 2 Results of RIEMS validation using our simulated sample dataset with original (upper half) and deviating (lower half) sequences

Input species	True positive	False positive	True negative	False negative	Unclassified	Sensitivity	Specificity	Positive predictive value	Negative predicitive value	Correct classification rate	False classification rate
Original sequences
Bacillus anthracis	12774	731	76880	0	0	100	99.06	94.59	100	99.19	0.81
Burkholderia mallei	16092	102	74129	62	0	99.62	99.86	99.37	99.92	99.82	0.18
Clostridium botulinum	12300	0	77649	436	0	96.58	100	100	99.44	99.52	0.48
Staphylococcus aureus	12425	0	77678	282	0	97.78	100	100	99.64	99.69	0.31
Escherichia coli	12289	0	77761	335	0	97.35	100	100	99.57	99.63	0.37
Yersinia pestis	12551	0	77788	46	0	99.63	100	100	99.94	99.95	0.05
Newcastle disease virus	418	0	89967	0	0	100	100	100	100	100	0
Akabane virus	119	0	90266	0	0	100	100	100	100	100	0
Influenza A virus	1	0	90384	0	0	100	100	100	100	100	0
Bos taurus	4906	0	85476	3	2	99.94	100	100	100	100	0
Canis lupus	5346	0	85039	0	0	100	100	100	100	100	0
Deviating sequences
Bacillus anthracis	12762	633	76978	12	0	99.91	99.18	95.27	99.98	99.29	0.71
Burkholderia mallei	16055	79	74152	99	0	99.39	99.89	99.51	99.87	99.8	0.2
Clostridium botulinum	12358	1	77648	378	0	97.03	100	99.99	99.52	99.58	0.42
Staphylococcus aureus	12484	1	77677	223	0	98.25	100	99.99	99.71	99.75	0.25
Escherichia coli	12400	0	77761	224	1	98.23	100	100	99.71	99.75	0.25
Yersinia pestis	12529	0	77788	68	1	99.46	100	100	99.91	99.92	0.08
Newcastle disease virus	418	0	89967	0	0	100	100	100	100	100	0
Akabane virus	119	0	90266	0	0	100	100	100	100	100	0
Influenza A virus	1	0	90384	0	0	100	100	100	100	100	0
Bos taurus	4887	0	85476	22	5	99.55	100	100	99.97	99.98	0.02
Canis lupus	5346	0	85039	0	0	100	100	100	100	100	0

ISSN: 1471-2105